Candidate loci

https://www.ncbi.nlm.nih.gov/nuccore/?term=Cannabis%20ALT4

https://www.ncbi.nlm.nih.gov/search/all/?term=Cannabis%20BKR

Methods

Genome Wide Association Study

In order to discover variants associated with the varin phenotype, a Genome Wide Association Study (GWAS) was performed using GAPIT3 (https://doi.org/10.1016/j.gpb.2021.08.005). The varin data was ordered quantile (ORQ) normalization transformed using the ‘bestNormalize::orderNorm()’ function (10.32614/RJ-2021-041; 10.1080/02664763.2019.1630372) to improve normalcy. Genotypic data in the VCF format (https://doi.org/10.1093/bioinformatics/btr330) was imported into R (https://www.R-project.org/) using vcfR (https://doi.org/10.1111/1755-0998.12549) and converted to hapmap format using vcfR::vcfR2hapmap(). The ordered quantile normalized phenotypes and the hapmap format genotypes were used for GWAS using the function GAPIT::GAPIT() and the options PCA.total = 6 and model = “Blink”. The Blink model begins with a simple model where the phenotype is described as a function of the dosage of the alternate allele in the genotypes. These are sorted by p-value. The first variant is selected subsequent loci that are determined to be in linkage disequilibrium with the first are removed. This is iterated through subsequent variants until the remaining variants are all organized by linkage. Detail on the Blink method can be found in it’s publication (https://doi.org/10.1093/gigascience/giy154).

Figure X. Manhattan plot exploring genome wide genotype association with the phenotypic trait ‘varin content’. Points indicated the genomic location and significance of association for each variant. The size and transparency of each point was scaled by it’s significance.

Phenotypes

PCA

A caption

A caption

Manhattan plots

## [1] "pca3_BLINK.Varin_Total"       "pca6_BLINK.Varin_Total"      
## [3] "pca6_Blink, OrderNorm_Varin"  "pca9_BLINK.Varin_Total"      
## [5] "pca10_BLINK, Varin"           "pca10_BLINK, OrderNorm_Varin"
## [7] "pca20_BLINK.Varin_Total"
## [1] TRUE

Table X. Select results from GAPIT GWAS using the Blink model, sorted by P.value.
SNP P.value -log10(P) MAF nobs H.B.P.Value Effect POS Pos
EH23b.chrX_44482355 0.0e+00 14.363844 0.3907407 270 0.0000000 10.051960 697415769 44482355
EH23b.chr7_290840 0.0e+00 9.941508 0.4425926 270 0.0000053 3.088768 467410754 290840
EH23b.chr4_67626398 0.0e+00 8.282825 0.4870370 270 0.0001621 5.739319 295311024 67626398
EH23b.chr9_19245258 0.0e+00 7.428058 0.4907407 270 0.0008700 -2.803471 606227672 19245258
EH23b.chr4_34229722 1.4e-06 5.848023 0.4962963 270 0.0264643 5.163312 261914348 34229722
EH23b.chr4_71883653 5.0e-06 5.304251 0.4796296 270 0.0708253 6.647073 299568279 71883653
EH23b.chr4_34229716 5.3e-06 5.274367 0.4981481 270 0.0708253 4.749994 261914342 34229716
EH23b.chr6_29171329 8.3e-06 5.081324 0.4740741 270 0.0857479 -4.846044 416278465 29171329
EH23b.chr6_63911547 8.5e-06 5.073016 0.3425926 270 0.0857479 4.501584 451018683 63911547
EH23b.chr6_29171313 9.2e-06 5.036430 0.4685185 270 0.0857479 4.727768 416278449 29171313

Loop

PCA = 6

## [1]  20 255
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